The Day Molly Hooper Died
by MacyBear17
Summary: These few scribbled words had managed to do what even two years of lying to her friends and worrying about Sherlock Holmes all by herself had failed to do. These words robbed her of the hope that had kept her going.


_**A/N: I know, I know. There are a lot of other stories I should be updating. But this just wouldn't let me go!**_

 _ **Please don't forget to review your thoughts and ideas.**_

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Molly Hooper sat at the window seat of her tiny London flat, her eyes staring sightlessly onto the rain slicked streets. It was New Year's Day, but it felt to the pathologist as if someone had leached all the colors from her world. From her limp hand, hung a piece of paper with just a few lines of sharp black letters scribbled on it.

Those words, those few words had managed to do to Molly what even two years of lying to her friends and silently mourning Sherlock Holmes on her own had never done. Because then, she had hope. Hope that she would see Sherlock once more. But with these few words, that hope had been torn away from her.

Molly wondered if it would've been kinder had she never known, but dismissed the idea as soon as it formed.

She'd not known anything was going on till today. She knew that they'd all spent Christmas day with Sherlock's parents and she hadn't even given a second thought to not being invited. Of course, even when Sherlock had told her that she mattered, Molly Hooper knew that she meant nothing more than a competent pathologist to the consulting detective most of the time. So, she'd spent another Christmas with just Toby for company, indulging in an excess of eggnog and watching more Christmas specials than she should have.

The first inkling that something was up came with the newspapers on Boxing Day… They carried the headlines of the death of Charles Augustus Magnussen. Trying to get in touch with Sherlock or Mycroft had proved futile. When she'd been unable to get in touch with any of them, neither the Watsons nor Lestrade or even Mrs. Hudson, Molly had started to panic.

She'd tried to convince herself that if something truly awful had happened, her friends would tell her. But the incident with Sherlock getting shot through the gut and her having to find out about it through the ER nurse who was her friend, flashed through her mind and it was all Molly Hooper could do to stop from pulling her own hair out of its roots in frustration and fear for her friends.

The next few days had been the longest in Molly's life. Not knowing was worse emotional torture than knowing the situation would've been. In desperation, Molly finally called the one number on her phone that she'd never dialed before. It was the number given to her by Anthea, Mycroft's girl Friday, during the days of Sherlock's faked death. Anthea had taken one look at Molly's pathetic expression the day after Sherlock's jump and told her to call the number if she wanted to talk. While the offer was made genuinely, Molly had never made the call.

Even that attempt was wasted as the only reaction she got from her phone was a mechanized female voice telling her to check the number she'd dialed.

New Year's Day early morning had found Molly Hooper exhausted from lack of sleep or food and emotionally distraught from worrying about the worst possible outcomes, which might've been why she almost didn't register her doorbell. Molly almost flew to the door, fighting the rising tide of hope that it might be one of her friends, better yet Sherlock himself at her door. But to her utter disappointment, all she found upon opening said door was an envelope hand addressed to her. The envelope itself was of excellent quality, it had no postal stamp on it and upon inspection, no return address either.

Curiosity and dread fighting for place in her heart, Molly carefully opened the seal on the envelope and pulled out a single sheet of thick, cream paper, hoping to see Sherlock's illegible scratches on it. Even if no one thought to come to her or tell her what was going on, if Sherlock had thought to write to her in the midst of it all, Molly Hooper was happy, relieved and curious all at once.

But even that hope was destined to be shattered as she spied a strong but decidedly female handwriting on the sheet of paper she clutched like a lifeline.

The moment the words on the paper registered in Molly's brain, had someone stood in front of her, they would've been able to see no discernible reaction from her other than the ever-present light in her eyes winking out of existence as surely as if someone had dropped a bucket of water on it. With those few soul sucking words, Anthea had destroyed Molly's entire existence.

* * *

 _ **Ms. Hooper,**_

 _ **As of 25th December, Mr. Sherlock Holmes was apprehended for the murder of Charles Augustus Magnussen. He had been in protective custody till the Government could make a decision about his sentence. On New Year's Day, he is being transported to Eastern Europe by private jet where he would undertake a six month long mission before being assassinated as per the orders of the British Government.**_

 _ **A. G.**_

 _ **Office of Intelligence**_

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Molly had been sat at the window seat for how long she didn't know and she didn't care. This time, the click of her front door unlocking did not even register in her grief laden brain. She knew it couldn't be Sherlock walking in through the doors and she didn't care who else it was.

The sight of the supposedly dead James Moriarty standing in front of her clad in his signature Westwood suit flanked by a tall and decidedly cruel looking man pointing a gun at her did surprisingly little to startle her.

Molly Hooper found that she was now beyond those little things called emotions. These last few days had wrung every last drop out of her and now all she was left with, was logic - cold, cruel and entirely dispassionate. It had taken the loss of Sherlock Holmes to make her into a version of him. But Molly knew that she could surpass even the world's only consulting detective at the moment. She had nothing to lose and didn't want to gain anything, which made her the most dangerous kind of opponent Jim Moriarty could go up against – the one who simply didn't care.

Which was probably why, when two days later, on the third of January, black suited agents broke open the door of Molly's tiny central London flat looking for one female corpse, they were presented with two male once instead, their bodies sliced open and sewn back cleanly, the work of a consummate professional pathologist. The only detail of note, were the perfectly tied red bows stuck onto each of their heads.

Mycroft Holmes, the last man to enter the flat, took one look at the corpses of James Moriarty and Sebastian Moran laid out on the carpet and for the first time in his life, he paled. With his usual powers of perception, the elder Holmes brother had surmised the situation in the two seconds he'd spent in the flat. That a tiny pathologist, completely untrained in the art of assassination had managed to subdue, kill and autopsy two of the world's worst criminals within 24 hours was beyond belief for even the most cynical and battle hardened official of the British Government.

Mycroft's lips tightened imperceptibly as he stooped down to gather the sheet of writing paper carelessly lying on the coffee table and with a slight nod, knew what he had to do.

Orders were issued to clear the scene immediately… This had never happened, they had never been here and these men had not seen what they saw in that flat today. James Moriarty and Sebastian Moran were his problems to deal with. The occurrences of today would be wiped from everyone's memories and no one would be mentioning Molly Hooper or the two bodies found in her flat ever again.

The next day, Anthea found herself put back into active field duty, a move she knew was imminent after the insubordination she had exhibited. She bit back whatever it was she'd meant to say to the Holmes brothers and walked out with her head held high.

John and Mary Watson, Lestrade and Mrs. Hudson were informed that due to the Moriarty broadcast and an imminent threat to her life, Molly Hooper had been moved to an undisclosed location with the witness protection program. No one doubted the word of Mycroft Holmes and for the next five and a half months, all was quiet.

* * *

At the end of his six month long mission, Sherlock Holmes found that he wasn't actually going to be executed. Almost disappointed, he returned to London to pick up where he'd left off. The welcome back party given by the Watsons was a great success. Lestrade, the Stamfords, Anderson and even Donovan had been invited. Billy Wiggins had flourished as the head of the Homeless Network during Sherlock's absence and he'd become a regular fixture at the Watsons', who liked to keep an eye on him. Mycroft had made a token appearance before scurrying off, muttering under his breath about starting another war.

It was almost a week after his return that Sherlock Holmes stepped into the lab at St. Bart's, clearly expecting to see Molly Hooper there. One could imagine his surprise when he came upon a completely reconfigured laboratory, with about five people working there, none of them the diminutive figure of his pathologist.

Upon inquiring(read : threatening) with Mike Stamford, Sherlock was informed that Molly Hooper had suddenly turned in her resignation due to personal reasons about half a year previously. The timing of her resignation struck Sherlock like a rock to the head and with a swish of his Belstaff, he was off to Mycroft's office.

The time it took to reach Mycroft's Whitehall office was spent in contemplations of how he could have forgotten his pathologist. Sherlock had noticed that she hadn't shown up to the party nor had anyone spoken about her or to her. Dread pooling in his gut, Sherlock hurried into his brother's office, with all intentions of shaking the answer out of the fatty, when he stopped at the resigned expression on Mycroft's face.

"She's gone isn't she?"

With a long suffering sigh, Mycroft pushed a file towards his brother. It was the official version of what had been found at Dr. Molly Hooper's flat on January 3rd. Sherlock slumped into the chair as he read of her body being found cut open with her own scalpel, tortured and killed by James Moriarty and his minion Sebastian Moran.

Mycroft Holmes knew, that in his own way, Sherlock held a lot of affection for the pathologist. He might not have been in love with her but he definitely loved her equally if not more than, his other so-called friends. Which was why, he knew that Sherlock could never know what had really been found at Dr. Hooper's house.

Sherlock had always been so passionate, so impulsive, so easily hurt. It had always been his responsibility to protect his younger brother and Mycroft knew he would continue to do so, even if it was to his own detriment. He had lost Anthea in the mess, but that couldn't be focused upon. All that was needed now, was to make sure Sherlock weathered this storm and never found out the truth.

If he had to divert Sherlock's attention whenever that new American assassin left them presents tied in perfect red bows, all of the bodies sliced and sewn back up perfectly, he would do so until his dying breath.

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 _ **A/N2 :**_

 _ **Aaand that's what came out of the thought banging around in my brain for quite some time. Hope you liked it!**_

 _ **Please don't forget to review your thoughts and opinions. I would love to hear from you guys!**_

 _ **Love and XXX**_


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